Thu, 02 Aug 2012

New package mlica2 with initial version 1.0
Package: mlica2
Type: Package
Title: Independent Component Analysis using Maximum Likelihood
Version: 1.0
Date: 2012-07-17
Author: Andrew Teschendorff
Maintainer: Thomas Nelson
Description: An R code implementation of the maximum likelihood (fixed point) algorithm of Hyvaerinen, Karhuna, and Oja for independent component analysis.
License: GPL-2
Packaged: 2012-08-02 14:49:57 UTC; tnelson
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2012-08-02 19:26:19

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Package fanplot updated to version 1.1 with previous version 1.0 dated 2012-07-17

Title: Visualisations of sequential probability distributions.
Description: The fanplot package contains a collection of R functions to effectively display plots of sequential distributions such as probabilistic forecasts. The plotting of distributions are based around two functions. The first, pn, calculates the percentiles for a set of sequential distributions over a specified time period. The second, fan, plots the calculated percentiles of the sequential distributions. The resulting plot is a set of coloured polygon, with shadings corresponding to the percentile values.
Author: Guy J. Abel
Maintainer: Guy J. Abel

Diff between fanplot versions 1.0 dated 2012-07-17 and 1.1 dated 2012-08-02

 fanplot-1.0/fanplot/data/ew.mcmc.rda       |only
 fanplot-1.0/fanplot/man/ew.mcmc.Rd         |only
 fanplot-1.0/fanplot/model                  |only
 fanplot-1.1/fanplot/DESCRIPTION            |   25 +-
 fanplot-1.1/fanplot/MD5                    |   39 ++--
 fanplot-1.1/fanplot/R/fanplot-internal.R   |  251 ++++++++++++++---------------
 fanplot-1.1/fanplot/R/pn.R                 |    4 
 fanplot-1.1/fanplot/data/datalist          |    4 
 fanplot-1.1/fanplot/data/pnew.mcmc.rda     |only
 fanplot-1.1/fanplot/data/rnew.mcmc.rda     |only
 fanplot-1.1/fanplot/data/th.mcmc.rda       |binary
 fanplot-1.1/fanplot/data/y.mcmc.rda        |only
 fanplot-1.1/fanplot/inst                   |only
 fanplot-1.1/fanplot/man/fan.Rd             |   59 +++---
 fanplot-1.1/fanplot/man/fan.fill.Rd        |    9 -
 fanplot-1.1/fanplot/man/fan.txt.Rd         |   18 +-
 fanplot-1.1/fanplot/man/fanplot-package.Rd |    6 
 fanplot-1.1/fanplot/man/pn.Rd              |   45 +++--
 fanplot-1.1/fanplot/man/pnew.mcmc.Rd       |only
 fanplot-1.1/fanplot/man/rnew.mcmc.Rd       |only
 fanplot-1.1/fanplot/man/svpdx.Rd           |   16 +
 fanplot-1.1/fanplot/man/th.mcmc.Rd         |   10 -
 fanplot-1.1/fanplot/man/y.mcmc.Rd          |only
 23 files changed, 263 insertions(+), 223 deletions(-)

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Package basicspace updated to version 0.06 with previous version 0.05 dated 2012-01-17

Title: A Package to Recover a Basic Space from Issue Scales
Description: Conducts Aldrich-McKelvey and Blackbox Scaling to Recover Latent Dimensions of Judgment
Author: Keith Poole , Howard Rosenthal , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: James Lo

Diff between basicspace versions 0.05 dated 2012-01-17 and 0.06 dated 2012-08-02

 basicspace-0.05/basicspace/data/.Rapp.history      |only
 basicspace-0.06/basicspace/DESCRIPTION             |   14 
 basicspace-0.06/basicspace/HISTORY                 |   15 
 basicspace-0.06/basicspace/MD5                     |   12 
 basicspace-0.06/basicspace/R/basicspace.R          |    7 
 basicspace-0.06/basicspace/inst/doc/basicspace.Rnw |  350 +++++++++++----------
 basicspace-0.06/basicspace/inst/doc/basicspace.bib |   31 +
 basicspace-0.06/basicspace/inst/doc/basicspace.pdf |binary
 8 files changed, 243 insertions(+), 186 deletions(-)

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Package truncnorm updated to version 1.0-6 with previous version 1.0-5 dated 2011-03-22

Title: Truncated normal distribution
Description: r/d/p/q functions for the truncated normal distribution
Author: Heike Trautmann and Detlef Steuer and Olaf Mersmann and Björn Bornkamp
Maintainer: Olaf Mersmann

Diff between truncnorm versions 1.0-5 dated 2011-03-22 and 1.0-6 dated 2012-08-02

 truncnorm-1.0-5/truncnorm/inst            |only
 truncnorm-1.0-5/truncnorm/tests/RUnit.R   |only
 truncnorm-1.0-6/truncnorm/DESCRIPTION     |   10 ++++------
 truncnorm-1.0-6/truncnorm/MD5             |only
 truncnorm-1.0-6/truncnorm/src/truncnorm.c |   22 ++++++++++++++--------
 truncnorm-1.0-6/truncnorm/src/zeroin.c    |only
 truncnorm-1.0-6/truncnorm/src/zeroin.h    |only
 7 files changed, 18 insertions(+), 14 deletions(-)

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Package CompetingRiskFrailty (with last version 2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2007-11-26 2.0
2006-08-11 1.0

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Package TwoWaySurvival (with last version 2.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2007-11-27 2.2
2007-11-24 2.1
2006-10-28 2.0

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Package phangorn updated to version 1.6-4 with previous version 1.6-3 dated 2012-07-01

Title: Phylogenetic analysis in R
Description: Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep

Diff between phangorn versions 1.6-3 dated 2012-07-01 and 1.6-4 dated 2012-08-02

 DESCRIPTION                    |    8 ++--
 MD5                            |   10 ++---
 R/phylo.R                      |   38 +++++++++++++++++++--
 inst/doc/Trees.pdf             |binary
 inst/doc/phangorn-specials.pdf |binary
 src/phangorn.c                 |   71 ++++++++++++++++++++++++-----------------
 6 files changed, 85 insertions(+), 42 deletions(-)

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New package GOSim with initial version 1.2.7.2
Package: GOSim
Version: 1.2.7.2
Date: 2012-08-01
Title: Computation of functional similarities between GO terms and gene products; GO enrichement analysis
Author: Holger Froehlich
Maintainer: Holger Froehlich
Depends: R (>= 2.7.0), GO.db (>= 2.2.0), AnnotationDbi, annotate, topGO, cluster (>= 1.11.7), flexmix, RBGL, graph, Matrix, corpcor, org.Hs.eg.db, igraph0
LazyLoad: Yes
Description: This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis
License: GPL (>= 2)
URL: www.cran.r-project.org
Packaged: 2012-08-02 07:41:46 UTC; frohlich
Repository: CRAN
Date/Publication: 2012-08-02 09:33:13

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Package sspir updated to version 0.2.10 with previous version 0.2.9 dated 2012-07-13

Title: State Space Models in R
Description: A glm-like formula language to define dynamic generalized linear models (state space models). Includes functions for Kalman filtering and smoothing. Estimation of variance matrices can be performed using the EM algorithm in case of Gaussian models. Read help(sspir) to get started.
Author: Claus Dethlefsen, \enc{Søren}{Soren} Lundbye-Christensen and Anette Luther Christensen
Maintainer: Claus Dethlefsen

Diff between sspir versions 0.2.9 dated 2012-07-13 and 0.2.10 dated 2012-08-02

 CHANGES                |    5 
 DESCRIPTION            |    8 
 MD5                    |   28 -
 NAMESPACE              |    1 
 R/EMalgo.R             |  146 +++----
 R/SS.R                 |   47 +-
 R/forecast.R           |only
 R/kfs.R                |   10 
 data/kurit.rda         |binary
 data/mumps.rda         |binary
 data/mumps.txt.gz      |binary
 data/vandrivers.rda    |binary
 data/vandrivers.txt.gz |binary
 man/EMalgo.Rd          |    4 
 man/forecast.Rd        |only
 sspir-Ex.R             |  971 +++++++++++++++++++++++++------------------------
 16 files changed, 656 insertions(+), 564 deletions(-)

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Package OOmisc updated to version 1.1 with previous version 1.0 dated 2012-04-11

Title: Ozgur-Ozlem Miscellaneous
Description: Includes miscellaneous functions.
Author: Ozgur Asar, Ozlem Ilk
Maintainer: Ozgur Asar

Diff between OOmisc versions 1.0 dated 2012-04-11 and 1.1 dated 2012-08-02

 DESCRIPTION   |    8 ++++----
 MD5           |   16 +++++++++++-----
 NAMESPACE     |    5 +++++
 R/ePCP.R      |only
 R/expit.R     |only
 R/newton.R    |    4 ++--
 R/nll.R       |only
 man/OOmisc.Rd |   12 ++++++------
 man/ePCP.Rd   |only
 man/expit.Rd  |only
 man/newton.Rd |   13 ++++++++-----
 man/nll.Rd    |only
 12 files changed, 36 insertions(+), 22 deletions(-)

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Package Metadata updated to version 1.1 with previous version 1.0 dated 2011-09-19

Title: Collates Metadata for Climate Surface Stations
Description: This package collects and downloads a variety of open GIS datasets that can be used to characterize the surface properties of Latitude/Longitude points. In addition, some restricted ( registration required to download) datasets are processed. Dataset include: distance from coast, distance from airport, land cover, land use, population density, historical populations, nightlights, impermable surfaces,urban extent, irrigation, and blue water use.
Author: Steven Mosher
Maintainer:

Diff between Metadata versions 1.0 dated 2011-09-19 and 1.1 dated 2012-08-02

 DESCRIPTION             |    8 ++++----
 MD5                     |    7 ++++---
 demo/00Index            |    2 ++
 demo/Landmask.R         |only
 man/Metadata-package.Rd |    2 +-
 5 files changed, 11 insertions(+), 8 deletions(-)

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Package gMCP updated to version 0.7-12 with previous version 0.7-11 dated 2012-07-21

Title: Graph Based Multiple Comparison Procedures
Description: This package provides functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests, adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer

Diff between gMCP versions 0.7-11 dated 2012-07-21 and 0.7-12 dated 2012-08-02

 DESCRIPTION                                               |    6 
 MD5                                                       |   45 +-
 NEWS                                                      |   17 
 R/gMCP.R                                                  |    8 
 R/misc.R                                                  |   64 +++
 R/subVariables.R                                          |    6 
 TODO                                                      |    7 
 inst/doc/AQuickStart.pdf                                  |binary
 inst/doc/gMCP.pdf                                         |binary
 inst/doc/parametric.pdf                                   |binary
 inst/java-src/org/af/gMCP/config/VersionComparator.java   |    9 
 inst/java-src/org/af/gMCP/gui/CreateGraphGUI.java         |    3 
 inst/java-src/org/af/gMCP/gui/ErrorDialogGMCP.java        |  267 +++++++++++++-
 inst/java-src/org/af/gMCP/gui/RControl.java               |    5 
 inst/java-src/org/af/gMCP/gui/ReproducableLog.java        |only
 inst/java-src/org/af/gMCP/gui/graph/EdgeWeight.java       |    2 
 inst/java-src/org/af/gMCP/gui/graph/GraphView.java        |    1 
 inst/java-src/org/af/gMCP/gui/graph/NetList.java          |   33 +
 inst/java-src/org/af/gMCP/gui/graph/NetListPopUpMenu.java |    4 
 inst/java-src/org/af/gMCP/gui/graph/PPanel.java           |    6 
 inst/java-src/org/af/gMCP/gui/graph/PView.java            |    3 
 inst/java-src/tests/InteractionTest.java                  |    4 
 inst/java-src/tests/PPanelTest.java                       |    9 
 inst/java/gsrmtp.jar                                      |binary
 24 files changed, 439 insertions(+), 60 deletions(-)

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Package crn updated to version 1.1 with previous version 1.0 dated 2011-09-21

Title: Downloads and Builds datasets for Climate Reference Network
Description: The crn package provides the core functions required to download and format data from the Climate Reference Network. Both daily and hourly data are downloaded from the ftp, a consolidated file of all stations is created, station metadata is extracted. In addition functions for selecting individual variables and creating R friendly datasets for them is provided.
Author: Steven Mosher
Maintainer: Steven Mosher

Diff between crn versions 1.0 dated 2011-09-21 and 1.1 dated 2012-08-02

 DESCRIPTION        |    8 ++++----
 MD5                |    4 ++--
 man/crn-package.Rd |    2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

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New package coexist with initial version 1.0
Package: coexist
Type: Package
Title: Species coexistence modeling and analysis
Version: 1.0
Date: 2012-08-01
Author: Youhua Chen
Maintainer: Youhua Chen
Description: species coexistence modeling under asymmetric dispersal and fluctuating source-sink dynamics;testing the proportion of coexistence scenarios driven by neutral and niche processes
License: GPL (>= 2.0)
Packaged: 2012-08-01 21:00:15 UTC; Owner
Repository: CRAN
Date/Publication: 2012-08-02 04:37:19

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